Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RELA

Cell type

Cell type Class
Digestive tract
Cell type
HT-29
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HT29 cell line
antibody
anti-p65 (Cell signaling, #6956)
treatment
TNF
treatment time
4 hr

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were prepared from ~5 millon single cell dissociated of organoid cultures or monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies. Libraries were prepared using the NEXTflex ChIP-seq kit (Cat# NOVA-5143-02; PerkinElmer) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
10219005
Reads aligned (%)
95.8
Duplicates removed (%)
17.7
Number of peaks
192 (qval < 1E-05)

hg19

Number of total reads
10219005
Reads aligned (%)
95.6
Duplicates removed (%)
17.8
Number of peaks
232 (qval < 1E-05)

Base call quality data from DBCLS SRA